ncdfFlow 2.17.0
Mike Jiang
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ncdfFlow | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ncdfFlow_2.17.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ncdfFlow.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ncdfFlow/DESCRIPTION’ ... OK
* this is package ‘ncdfFlow’ version ‘2.17.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
src/libwin/i386/libhdf5ForBioC-7.dll src/libwin/i386/libsz-2.dll
src/libwin/x64/libhdf5ForBioC-7.dll src/libwin/x64/libsz-2.dll
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ncdfFlow’ can be installed ... [20s/20s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘flowCore’ ‘flowViz’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘ncdfFlow’ for: ‘rbind2’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘parallel’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘BH’ ‘RcppArmadillo’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
‘flowCore:::makeFCSparameters’ ‘flowCore:::readFCSgetPar’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ncdfFlowSet,flowSet: warning in assign(guid, new("flowFrame", exprs =
matrix(numeric(0), nrow = 0, ncol = 0), parameters(x[[guid]]),
description(x[[guid]])), env = e1): partial argument match of 'env'
to 'envir'
rbind2,ncdfFlowList-ANY : <anonymous> : <anonymous>: warning in
assign(curSample, NA, env = indiceEnv): partial argument match of
'env' to 'envir'
read.ncdfFlowSet: no visible global function definition for ‘mclapply’
Undefined global functions or variables:
mclapply
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run-all.R’ [7s/7s]
[7s/7s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/ncdfFlow.Rcheck/00check.log’
for details.
* installing *source* package ‘ncdfFlow’ ...
configure: No directory was specified for --with-hdf5. Trying to find hdf5 using pkg-config.
checking for pkg-config... /usr/bin/pkg-config
Package hdf5 was not found in the pkg-config search path.
Perhaps you should add the directory containing `hdf5.pc'
to the PKG_CONFIG_PATH environment variable
No package 'hdf5' found
configure: pkg-config was not able to find the hdf5 library.
configure: Trying some common locations."
configure: search for hdf5 library in: /usr/local/lib
configure: search for hdf5 library in: /usr/local/lib64
configure: search for hdf5 library in: /usr/local/lib/x86_64-linux-gnu
configure: search for hdf5 library in: /usr/local/lib64/x86_64-linux-gnu
checking for h5cc... /usr/bin/h5cc
configure: PKG_CPPFLAGS =
configure: PKG_LIBS = -lhdf5
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c bitOps.cpp -o bitOps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c hdfFlow.c -o hdfFlow.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c init.c -o init.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include" -fpic -g -O2 -c readFrame.cpp -o readFrame.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o ncdfFlow.so RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -lhdf5 -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/ncdfFlow.Rcheck/ncdfFlow/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘lapply’ from package ‘base’ in package ‘ncdfFlow’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ncdfFlow)